Functional roles of a tetraloop/receptor interacting module in a cyclic di-GMP riboswitch

Yuki Fujita, Takahiro Tanaka, Hiroyuki Furuta, Yoshiya Ikawa

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Riboswitches are a class of structural RNAs that regulate transcription and translation through specific recognition of small molecules. Riboswitches are attractive not only as drug targets for novel antibiotics but also as modular tools for controlling gene expression. Sequence comparison of a class of riboswitches that sense cyclic di-GMP (type-I c-di-GMP riboswitches) revealed that this type of riboswitch frequently shows a GAAA loop/receptor interaction between P1 and P3 elements. In the crystal structures of a type-I c-di-GMP riboswitch from Vibrio cholerae (the Vc2 riboswitch), the GNRA loop/receptor interaction assembled P2 and P3 stems to organize a ligand-binding pocket. In this study, the functional importance of the GAAA loop-receptor interaction in the Vc2 riboswitch was examined. A series of variant Vc2 riboswitches with mutations in the GAAA loop/receptor interaction were assayed for their switching abilities. In mutants with mutations in the P2 GAAA loop, expression of the reporter gene was reduced to approximately 40% - 60% of that in the wild-type. However, mutants in which the P3 receptor motif was substituted with base pairs were as active as the wild-type. These results suggested that the GAAA loop/receptor interaction does not simply establish the RNA 3D structure but docking of P2 GAAA loop reduces the flexibility of the GAAA receptor motif in the P3 element. This mechanism was supported by a variant riboswitch bearing a theophylline aptamer module in P3 the structural rigidity of which could be modulated by the small molecule theophylline.

Original languageEnglish
Pages (from-to)141-145
Number of pages5
JournalJournal of Bioscience and Bioengineering
Volume113
Issue number2
DOIs
Publication statusPublished - Feb 1 2012

Fingerprint

Riboswitch
RNA
Bearings (structural)
Molecules
Antibiotics
Transcription
Gene expression
Rigidity
Genes
Crystal structure
Ligands
Theophylline
bis(3',5')-cyclic diguanylic acid
Mutation
Vibrio cholerae
Reporter Genes
Base Pairing

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology

Cite this

Functional roles of a tetraloop/receptor interacting module in a cyclic di-GMP riboswitch. / Fujita, Yuki; Tanaka, Takahiro; Furuta, Hiroyuki; Ikawa, Yoshiya.

In: Journal of Bioscience and Bioengineering, Vol. 113, No. 2, 01.02.2012, p. 141-145.

Research output: Contribution to journalArticle

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